The i2b2 transmart Foundation Community Meeting

The i2b2 transmart Foundation Community Meeting January 15, 2019 11:00 AM Eastern Start Time 11:05 AM Eastern Meetings are recorded

Agenda 1 Welcome 5 Foundation Platform Overview 2 Preview of 2019 6 i2b2/transmart v18.1 Production Release 3 Harvard Symposium - June 2019 7 Working Groups Update 4 Foundation Sponsorship Program 8 Ontology Working Group Report

Agenda 1 Welcome Diane Keogh, Executive Director 5 Foundation Platform Overview 2 Preview of 2019 6 i2b2/transmart v18.1 Production Release 3 Harvard Symposium - June 2019 7 Working Groups Update 4 Foundation Sponsorship Program 8 Ontology Working Group Report

Foundation Activities: Preview of 2019 Community Meetings 3 rd Tuesday of every month at 11AM Eastern Single registration for all of the sessions Annual Meetings: Harvard Meeting: June 17-18 th, 2019 at Harvard Medical School European Meeting: planning Training Program last Friday of every month at 11AM Eastern Individual registration required for each session Scientific Conferences

2019 Training Program January No Session Planning in progress April i2b2 Training Ontology for beginners Partners Healthcare July i2b2 Training Install and Upgrade Partners Healthcare February TranSMART training using complex clinical dataset Rancho BioSciences May Glowing Bear and Visual Analytics with Fractalis The Hyve August In Planning March Basics of i2b2 U Kansas Med Ctr June TranSMART training using complex clinical dataset Rancho BioSciences September An overview of the 16.4 transmart Platform Axiomedix October In Planning November i2b2/transmart Platform DBMI/Harvard December In Planning

2019 Translational Science Meetings & Events Health Research Informatics, Jan 17, 2019, Utrecht, Netherlands Festival of Genomics, London, January 23-24, 2019, London, England ACTS - Translational Science 2019, March 5-8, 2019, Washington, DC Pistoia Annual European Conference 2019, March 13, 2019, London, UK AMIA 2019 INFORMATICS SUMMIT, MARCH 25-28, San Francisco CA AACR Annual Meeting, March 29- April 3, 2019, Atlanta, GA BioIT World, April 16-19, 2019, Boston, MA 3rd European Conference on Translational Bioinformatics (ECTB), April 16-17, 2019, Barcelona BioData West, October 9-11, 2019, San Diego, CA

Harvard Symposium 2019 Website

Contributing Sponsors Program Benefits of Contributing Sponsorship 2 free tickets to each foundation event Quarterly updates on the development roadmaps Access to early demonstrations Access to the high-priority JIRA tickets Contributing members will be recognized on the foundation website including a logo and brief description of research interests Mention in all event emails to attendees Mention in any i2b2 transmart Foundation publications and E-Blasts Acknowledgement during Foundation events Monthly Community Meeting acknowledgement\ What the Contributing Sponsors Program supports: Monthly community calls Monthly training programs Organization of the spring and fall conferences Operational support of the Project Management Committees Maintaining the foundation website Supporting the existing working groups and developing new groups User Group and other Foundation Events

2018 Contributing Sponsors

Foundation Platform Updates: January 2019 Platform Current Release I2b2 1.7.10 16.3 transmart 17.1 Server Only I2b2/tranSMART Preview Details of Next Release New License, Support for ACT Pic-Sure integration, Includes i2b2 1.7.7, transmart 16.4, PIC-SURE, Fractalis, Oracle Coming Next 1.7.11 16.4 Revised data model changes under discussion Updated Quickstart (Dec) First Production Release Soon

The i2b2 transmart Platform Environment I2b2 transmart Platform What is i2b2 transmart? An open source software platform for query and exploration of clinical, translational and genomics data What makes it different? Its modular ontology-driven architecture and community developed plugins and interfaces enable a variety of configurations to support the needs of data scientists, academic clinical investigators and industry

I2b2 transmart Platform 18.1 Final version of 18.1 Quickstart version available now Includes data loading options Production deployment coming soon

i2b2/transmart Searching

Genome-wide association study (GWAS) on cases vs controls

Foundation Working Groups User Interface led by Griffin Weber Ontologies led by Jim Campbell ETL led by Mike Mendis Use Cases Initial Members: Deb Batson, Lisa Bedford, Peter Rice, Kendra Elliston Operational Working Groups Events led by Rudy Potenzone Training led by Rudy Potenzone

I2b2/TranSMART Ontology Workgroup Jim Campbell

Workgroup Members Deb Batson Robert Bradford Jim Campbell Janice Donahoe Keith Elliston Farhan Hameed Mike Horvath Mary Helen Mays Mike Mendis Michelle Morris Victoria Morris Nitin Parikh Matvey Palchuk Lori Phillips Jay Pedersen Wibo Pipping Jeremy Provance Peter Rice Julianne Schneider Phillip Trevett Kavi Wagholikar Griffin Weber Donglu Xie

INITIAL CHARGE/DISCUSSION This group should try to reduce the level of difficulty of managing ontologies for the community. We need to identify and decide on the standards that are supported (endorsed by this group). We should develop a consolidated list of ontologies and decide as a group what should be the priority for focus. We should make this repository of ontologies available to the community via the foundation.

WIKI WORK PLAN http://community.i2b2.org/wiki/display/iwg/ontology+ Working+Group Ontology Basics Nitin Parikh (nbparikh@ucdavis.edu) Ontology Use Cases Diane Keogh (diane.keogh@transmartfoundation.org) Ontologies for Federated Networks Robert Bradford (Robert_Bradford@med.unc.edu) Ontology Tools Jim Campbell (Campbell@unmc.edu)

ONTOLOGY BASICS WORK PLAN http://community.i2b2.org/wiki/display/iwg/ontology+w orking+group Regular meetings past two months Draft of revised page prepared; procedures for review to be discussed

TOOLING WIKI WORK PLAN http://community.i2b2.org/wiki/display/iwg/ontology+working+ Group Draft for best practice guideline has had two rounds review: https://docs.google.com/document/d/1rhgvlkpduqx0uzbtl8hde6jhfv nrbwdnawncrt_ensm/edit NCBO tools: https://community.i2b2.org/wiki/display/ncbo/ontology+tools Plan to support standardized tools for building ONC standard ontologies; RxNorm/NDC_20181201 and ICD-10-CM_20181001 preparing for publication

PUBLISHED AND MAINTAINED I2B2 METADATA RESOURCES Accessible Research Commons for Health(ARCH): https://github.com/arch-commons/arch-ontology Accrual to Clinical Trials(ACT): https://github.com/dbmi-pitt/act-ontology SNOW_SHRINE: https://www.unmc.edu/pathology/informatics/tdc

ONTOLOGY NEEDS FOR TRANSMART?

Open Discussion

Thank You